phpDocumentor is not aware of conditional control structures because it would slow things down considerably. So, what phpDocumentor does is automatically ignore the second define and raise a warning. The warning can be eliminated with an @ignore tag on the second element like so:

If there are two files that contain the same procedural elements in the same package (for example, a common configuration file common.php), they will also be ignored as if they were in the same file. The reasoning behind this is simple. A package is an indivisible set of files and classes that a user will include in their code. Name conflicts must be avoided to allow successful execution.